Data cleaning and pre-processing
This section shows the main steps that have been applied to pre-process the raw data.
aCDOM spectra
The CDOM spectra were modelled according to the information in @.
acdom spectra were re-fitted using the complete data (i.e. between 350-500 nm) because the data in all_abs_transpose.txt started at 380 nm.
Average background values calculated between 683-687 nm and subtracted from each spectrum.
Some files were in binary format, so I could not open them (ex.: C2001000.YSA).
Some spectra start at 300 nm while others at 350 nm.
Calculated the correlation between the measured and the fitted values.
- Fits with R2 lower than 0.95 were removed from the data.
Absorption spectra with any negative values below 500 nm were removed.
Exported the complete spectra (350-700 nm): both the raw and the modelled data.
Phytoplankton and non-algal absorption
- Absorption spectra with any negative values below 500 nm were removed.
Irradiance
There were negative values in the irradiance data (Ed, Eu, Kd, Ku). I have cleaned the data by setting these negative values to NA.
Eu is in fact Eu0- that was estimated using a two-exponential function model.
Ed is in fact Ed0- calculated from 0.94 x ed0+.
There are differences in wavelengths among cruises. I have not found any information in the report concerning channel change across the missions.
| A2 |
C1 |
C3 |
C4 |
C5 |
C6 |
| 411 |
411 |
411 |
411 |
411 |
411 |
| 443 |
443 |
443 |
443 |
443 |
443 |
| 456 |
456 |
456 |
456 |
456 |
456 |
| 490 |
490 |
490 |
490 |
490 |
490 |
| 509 |
509 |
509 |
509 |
509 |
509 |
| 532 |
532 |
532 |
532 |
532 |
532 |
| 559 |
556 |
559 |
559 |
559 |
559 |
| 619 |
590 |
619 |
619 |
619 |
619 |
| 665 |
665 |
665 |
665 |
665 |
665 |
| 683 |
683 |
683 |
683 |
683 |
683 |
| 705 |
705 |
705 |
705 |
705 |
705 |
| 779 |
779 |
779 |
779 |
779 |
779 |
| 866 |
866 |
866 |
866 |
866 |
866 |
| A2 |
C1 |
C3 |
C4 |
C5 |
C6 |
| 559 |
556 |
559 |
559 |
559 |
559 |
| 619 |
590 |
619 |
619 |
619 |
619 |
Reflectance
- Reflectance values outside the 0-1 range were set to
NA.
Other stuff
- Extracted extra variables (
DOC, AQY) from Massimo 2000.
Bathymetry
- I have extracted the bathymetry at each sampling locations.
TODO
Use piggyback https://docs.ropensci.org/piggyback/
Release the final report PDF with a DOI and cite it in the main text.
- Who should be included in the release of this document?
Make sure that SPMR units are OK. um vs nm. Change accordingly in the SPMR code file (zzz_radiometer.R).
SPMR vertical profiles have been reprocessed. This means that the original surface data is not the same as the newly processed vertical profiles (i.e. extrapolation to the surface). How to deal with that?
References
Babin, Marcel. 2003.
“Variations in the Light Absorption Coefficients of Phytoplankton, Nonalgal Particles, and Dissolved Organic Matter in Coastal Waters Around Europe.” Journal of Geophysical Research 108 (C7): 3211.
https://doi.org/10.1029/2001JC000882.